uid=MCM,o=EDI,dc=edirepository,dc=org all public read metacommunity dynamics Eric Sokol sokole@gmail.com http://sokole.blogspot.com/ https://orcid.org/0000-0001-5952-0917 McMurdo Dry Valleys LTER http://mcmlter.org/ Inigo San Gil

Department of Biology, MSC03 2020 University of New Mexico Albuquerque NM 87131 US

(505) 277-2625 (505) 277-2541 isangil@lternet.edu data manager 2016-03-10 English

We use metacommunity simulations to understand how local and regional community assembly dynamics influence the regional biodiversity patterns that we observe in the McMurdo Dry Valleys ecosystem. A metacommunity refers to a network of communities in an ecosystem that are connected to one another by the dispersal of biota among sites. For example, ponds in the McMurdo Dry Valleys share common diatom species that are likely dispersed among neighboring ponds by wind. We have written a metacommunity model for the R programming language (MCSim, Sokol et al. 2015) to explore what biodiversity patterns look like for different metacommunity connectivity scenarios. This gives us the opportunity to model alternative hypotheses and explore how biodiversity metrics, such as beta-diversity, can be expected to respond to changing ecosystem connectivity for different sets of assumptions about the underlying dynamics that could potentially control biodiversity in the Dry Valleys. 

community dynamics diatoms dispersal modeling population and community properties simulation LTER Controlled Vocabulary

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https://mcm.lternet.edu/content/metacommunity-dynamics-simulations-diatoms-antarctic-ponds The Blue Lake North Lobe is in the Cape Roys area, In Ross Island.Code: BLNLNorth lobe of ice-covered  lake, <5 m  moat, area is about 41,529, at the time, the water temperature was about 6.3 degrees celsius. 166.176635742188 166.176635742188 -77.543998718262 -77.543998718262 The Blue Lake South Lobe is in the Cape Roys area, In Ross Island.Code: BLSLSouth lobe of ice-covered  lake, <1 m  moat, area is about 56,794 at the time, the water temperature was about 1.5 degrees celsius. 166.181732177734 166.181732177734 -77.545921325684 -77.545921325684 The Clear lake is an Ice-covered lake with ~33 % ice-free, in the Cape Roys area in Ross Island. The area the lake covers is about 10,929Code: CLLArea: 10,929 Measured Temperature: 2.9 166.161422729492 166.161422729492 -77.542182922363 -77.542182922363 The Coast Lake is a predominantly ice free lake in the Cape Roys area in Ross Island.Code : COLLake Area: 14,813 Temperature: 10.1   166.150375366211 166.150375366211 -77.542266845703 -77.542266845703 The Cape Royds Pond 1 is an ice free pond in the Ross IslandCode : CR1Area: 1,792 Temperature: 6.3 celsius  166.163772583008 166.163772583008 -77.552818298340 -77.552818298340 The Cape Roys Pond 2 is an ice-free pond at ROss Ilsand.Area 26Temperature: 6.2 celsiusCode: CRP2  166.177307128906 166.177307128906 -77.549003601074 -77.549003601074 The Cape Roys Pond 3 is in ROss Island, and is a predominantly ice free pond.Code: CRP3Area: 323Temperature: 5.4 celsius 166.172653198242 166.172653198242 -77.544097900391 -77.544097900391 The Cape Royds Pond 4 is located in Ross Island, predominantly ice-free with a snowbank.Code: CRP4Area 1692Temperature: 8 celsius 166.166946411133 166.166946411133 -77.543350219727 -77.543350219727 The Cape Royds Pond 5 is a small ice free pond in Ross IslandArea: 5Temperature : 9.1 166.158432006836 166.158432006836 -77.552848815918 -77.552848815918 The Cape Royds Pond 6 is a small ice-free pond at ROss Island.Code: CRP6Area: 897 Temperature: 8.9 celsius 166.172073364258 166.172073364258 -77.546722412109 -77.546722412109 The Green Lake is an ice-free pond, near coast Area: 3,020 Temperature : 9.4 Celsius 166.157424926758 166.157424926758 -77.549766540527 -77.549766540527 The Labyrinth Pond 4 is located in the Wright Valley. Ice-covered, heavily shaded, lense-shaped.Code: LAB4Area: 25,805Temperature: 2.6 celsius  161.063613891602 161.063613891602 -77.560478210449 -77.560478210449 A pond, 0.3 nautical miles (0.6 km) long, located 0.5 nautical miles (1 km) south of the snout of Commonwealth Glacier in Taylor Valley, Victoria Land, Antarctica. The pond is part of the Aiken Creek system and receives drainage from several glaciers including Commonwealth Glacier, Wales Glacier and the unnamed glacier next westward. 163.313079833984 163.328353881836 -77.597686767578 -77.598609924316 20 20 meter The Kaki Pond 3 is an ce-covered pond with a moat less than a meter. It is in the Taylor Bonney, looks like the Bonney Basin.Code: MP3Area:5,318Temperature:  162.711425781250 162.711425781250 -77.700569152832 -77.700569152832 The Kaki Pond 4 is located in the uplands of the Boney Basin, in the Taylor Valley, is ice covered with a moat less than a meter.Code: MP4Area:14,012 Temperature: 2.4 celsius   162.716186523438 162.716186523438 -77.696022033691 -77.696022033691 The McMurdo Hut Ridge Lower Pond is on Ross Island, small Ice-free, lense-shaped pond.Code: MCMLArea: 5Temperature: 8.6 166.644607543945 166.644607543945 -77.843482971191 -77.843482971191 The McMurdo Hut Ridge Upper Pond is an Ice-free, lense-shaped pond on Ross IslandArea: 393 Temperature: 6.3 celsius  166.645034790039 166.645034790039 -77.841217041016 -77.841217041016 The Nussbaum Riegel Pond is in the Taylor Valley in between the Bonney and Chad Basins.  An Ice-covered, oval pond.Code: NRP Area: 6,133 Temperature: 3.1 celsius 162.814727783203 162.814727783203 -77.684379577637 -77.684379577637 The Parera Pond is an Ice-covered, <1 m moat in the Taylor ValleyCode: PPArea:39,916 Temperature: 5.7 celsius 162.913177490234 162.913177490234 -77.654182434082 -77.654182434082 The Picture Pond is a former channel, oval pond in the Taylor Valley, near Explorer's Cove and Commonwealth GlacierCode PIPArea: 8,119 Temperature: 7.1 163.423706054688 163.423706054688 -77.588279724121 -77.588279724121 The Spaulding Pond is Mostly ice-free, circular and near Howard glacier in Taylor ValleyCode: SPP Area: 68,329 Temperature 9.9 celsius 163.123352050781 163.123352050781 -77.658096313477 -77.658096313477 The Pony Lake is an Ice-covered with moat, circular pond near Cape Royds in Ross IslandCode : POLArea: 9,974Temperature 4 celsius 166.167205810547 166.167205810547 -77.552848815918 -77.552848815918 2014-03-01 2015-03-02 Modeling code is managed in github, and the data output snapshots are stored here.   McMurdo Dry Valleys LTER http://mcmlter.org/ McMurdo Dry Valleys LTER http://mcmlter.org/ McMurdo Dry Valleys LTER

Field Sample Analysis and Model Approach We are parameterizing metacommunity simulations by using observational data collected across various MCM core experiments to characterize local habitat characteristics and the composition of biotic communities in aquatic and terrestrial habitats. For example, we have modeled different metacommunity scenarios based on the diatom communities observed in microbial mats sampled in ponds on Ross Island and in the McMurdo Dry Valleys (observational data described in Sakaeva et al. 2016). For each pond, we have measured a suite of environmental variables (e.g., pH, conductivity, nutrient concentrations) and recorded GPS locations. Similar to the modeling approach described by Sokol et al. (2015), we use the pond GPS coordinates to create a network of ponds in 2-dimensional space for the metacommunity simulations. We use the first axis of a principal component analysis (PCA) of pond environmental variables to create a composite environmental variable, used to characterize the local habitat at each pond in a simulation scenario. Diatom counts from cores collected from microbial mats from each pond were used to set the initial metacommunity conditions for all simulation scenarios. Similarly, we are also using this approach to understand the importance of connectivity for biodiversity data collected in nematode and soil bacteria studies at the MCM LTER.    Modeling code used: MCSim for the R statistical language. Latest version available on Github at https://github.com/sokole/MCSim (version used for this work is https://github.com/sokole/MCSim/releases/tag/v0.4.1.9001) Data Input Files The input files used for the Metacommunities simulations, all the empirical data used are included in a Zip file (see above). Four csv files contain information on the communities densities. These include the following taxa (coded): Ataylor, Ccymat, Claevis, Cmolest, Fpellic, Holigot, Hantzsc, Habundan, Hamphiox, Hmuelle, Helongat, Humidoph, Hhyperaus, Haustral, Hparall, Lutico, Laustro, Ldolia, Lgauss, Llaeta, Levolut Lmuticop LmLevk, LmWest, Lpermutic, Lvermeu Matomu Mpermit Mvar1, Mueller Mmerid Msupra, Mperaus, Nseibig, Nshack Ngrega Nlineo, Ncommu, Nwesto, Ppapil, Slatis, Lunknown, Cheam1Input locations are in two files, including UTM coordinates as well as Lat/Lon coordinates. The lake index serves as linkage for chemical, physical and taxa data. The pond or lakes chemistry empirical inputs include concentrations for Calcium, Iron, Chlorine, Bromine, Phosphates, Nitrites, Nitrates, Sulfates, Dissolved Organic Carbon and Amonia. Physical paramenters like the pH, the Conductivity and Temperature. Data Output Files Output files for example metacommunity simulations. Simulation results include species counts for each timestep from two different simulation scenarios. Example R code necessary to run these simulation scenarios is included R-code.  Best refer to github link, but here  an example for Diatoms is included in the Output ZIP file.  Eric provided you with a nice tutorial on how to use the MCSim simulation, follow it at: http://rpubs.com/sokole/159425

Metacommunities Data INPUTs These are example input files used for the Metacommunities simulations, all the empirical data used.Four csv files contain information on the communities densities, UTM coordinates as well as Lat/Lon coordinates  DATA_IN.zip 9433 application/zip https://mcm.lternet.edu/sites/default/files/data/DATA_IN.zip undefined Metacommunities Data OUTPUTS and code example Files on simulated community dynamics results as species counts. Includes code example. SIM_OUTPUT_MCM-diatom-examples.zip 721240 application/zip https://mcm.lternet.edu/sites/default/files/data/SIM_OUTPUT_MCM-diatom-examples_0.zip undefined